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- PDB-6ded: Crystal structure of the C-terminal ARM domain of Homo sapiens SP... -

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Basic information

Entry
Database: PDB / ID: 6ded
TitleCrystal structure of the C-terminal ARM domain of Homo sapiens SPIN90 (SH3-protein interacting with Nck), residues 351-722
ComponentsNCK-interacting protein with SH3 domain
KeywordsENDOCYTOSIS / inactive form / N-terminally truncated SPIN90 / 6 and 2-3 armadillo repeats / unable to activate Arp2-3 complex
Function / homology
Function and homology information


Arp2/3 complex binding / intermediate filament / RHO GTPases Activate WASPs and WAVEs / cytoskeleton organization / cytoskeletal protein binding / FCGR3A-mediated phagocytosis / positive regulation of neuron projection development / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / endocytosis ...Arp2/3 complex binding / intermediate filament / RHO GTPases Activate WASPs and WAVEs / cytoskeleton organization / cytoskeletal protein binding / FCGR3A-mediated phagocytosis / positive regulation of neuron projection development / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / endocytosis / nucleus / cytosol
Similarity search - Function
SPIN90, SH3 domain / SPIN90/Ldb17, leucine-rich domain / SPIN90/Ldb17 / SPIN90/Ldb17, leucine-rich domain / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
NCK-interacting protein with SH3 domain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 Å
AuthorsNolen, B.J. / Luan, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)R01GM092917 United States
CitationJournal: EMBO J. / Year: 2018
Title: Structure of the nucleation-promoting factor SPIN90 bound to the actin filament nucleator Arp2/3 complex.
Authors: Luan, Q. / Liu, S.L. / Helgeson, L.A. / Nolen, B.J.
History
DepositionMay 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NCK-interacting protein with SH3 domain
B: NCK-interacting protein with SH3 domain


Theoretical massNumber of molelcules
Total (without water)84,5822
Polymers84,5822
Non-polymers00
Water5,819323
1
A: NCK-interacting protein with SH3 domain


Theoretical massNumber of molelcules
Total (without water)42,2911
Polymers42,2911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NCK-interacting protein with SH3 domain


Theoretical massNumber of molelcules
Total (without water)42,2911
Polymers42,2911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.365, 76.170, 92.257
Angle α, β, γ (deg.)90.00, 93.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NCK-interacting protein with SH3 domain / 54 kDa VacA-interacting protein / 54 kDa vimentin-interacting protein / VIP54 / 90 kDa SH3 protein ...54 kDa VacA-interacting protein / 54 kDa vimentin-interacting protein / VIP54 / 90 kDa SH3 protein interacting with Nck / AF3p21 / Dia-interacting protein 1 / DIP-1 / Diaphanous protein-interacting protein / SH3 adapter protein SPIN90 / WASP-interacting SH3-domain protein / WISH / Wiskott-Aldrich syndrome protein-interacting protein


Mass: 42291.148 Da / Num. of mol.: 2 / Fragment: UNP residues 350-722
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCKIPSD, AF3P21, SPIN90 / Plasmid: pGv67
Details (production host): N-terminal GST-fusion with TEV cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9NZQ3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM Tris, pH 7.5, 700 mM sodium potassium tartrate
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9797423 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 3, 2016 / Details: Sagitally focusing 2nd crystal
RadiationMonochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797423 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 53032 / % possible obs: 99.3 % / Redundancy: 4.7 % / Biso Wilson estimate: 47.5 Å2 / Rpim(I) all: 0.087 / Rrim(I) all: 0.147 / Rsym value: 0.131 / Χ2: 2.374 / Net I/σ(I): 18
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2657 / CC1/2: 0.302 / Χ2: 1.356 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-30002.3.10data reduction
HKL-30002.3.10data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD model

Resolution: 2.204→35.699 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.65
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 2559 4.83 %random selection
Rwork0.2148 ---
obs0.216 52992 98.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.204→35.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5363 0 0 323 5686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035468
X-RAY DIFFRACTIONf_angle_d0.5957413
X-RAY DIFFRACTIONf_dihedral_angle_d12.3272037
X-RAY DIFFRACTIONf_chiral_restr0.022868
X-RAY DIFFRACTIONf_plane_restr0.003948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.204-2.24640.41051140.32742681X-RAY DIFFRACTION93
2.2464-2.29220.31491400.29632766X-RAY DIFFRACTION100
2.2922-2.3420.34351220.29132803X-RAY DIFFRACTION99
2.342-2.39650.34491140.26952834X-RAY DIFFRACTION99
2.3965-2.45640.30881640.26632774X-RAY DIFFRACTION99
2.4564-2.52280.29791460.25482777X-RAY DIFFRACTION100
2.5228-2.59710.30291250.25072835X-RAY DIFFRACTION100
2.5971-2.68080.27251490.24452797X-RAY DIFFRACTION100
2.6808-2.77660.26381480.23622826X-RAY DIFFRACTION100
2.7766-2.88780.2461330.22932824X-RAY DIFFRACTION100
2.8878-3.01910.25611160.2272846X-RAY DIFFRACTION100
3.0191-3.17820.24511510.2232827X-RAY DIFFRACTION100
3.1782-3.37720.24071710.21442774X-RAY DIFFRACTION100
3.3772-3.63770.20851710.19152817X-RAY DIFFRACTION100
3.6377-4.00330.20761650.1872801X-RAY DIFFRACTION99
4.0033-4.58160.19851420.17672817X-RAY DIFFRACTION99
4.5816-5.76840.21291380.19662866X-RAY DIFFRACTION100
5.7684-35.70340.2231500.19562768X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -17.2927 Å / Origin y: 7.3402 Å / Origin z: -23.7301 Å
111213212223313233
T0.2548 Å2-0.0145 Å20.0265 Å2-0.237 Å2-0.0229 Å2--0.2657 Å2
L0.4259 °2-0.0257 °20.3828 °2-0.253 °2-0.1799 °2--0.5256 °2
S-0.0434 Å °0.0309 Å °0.0196 Å °-0.0191 Å °0.0078 Å °-0.0293 Å °-0.0168 Å °0.0084 Å °0.0354 Å °
Refinement TLS groupSelection details: all

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